TU Delft

SUPPORT MATERIAL FOR PUBLICATIONS



Interactive demonstration of a biofilm model program

A java applet showing an interactive 2D monospecies biofilm model:


Run a monospecies 2D biofilm model
images/2007_Xavier_EnvSciTechnol.jpg Xavier JB, de Kreuk MK, Picioreanu C, van Loosdrecht MCM (2007) Multi-scale individual-based model of microbial and bioconversion dynamics in aerobic granular sludge
Environmental Science and Technology, 41 (18): 6410-6417.
images/2007_Picioreanu_WaterResearch.jpg Picioreanu C, Head IM, Katuri KP, Van Loosdrecht MCM, Scott K (2007) A computational model for biofilm-based microbial fuel cells
Water Research, 41(13):2921-2940.
images/2007_Picioreanu_WatSciTechnol.jpg
Picioreanu C, Kreft J-U, Klausen M, Haagensen JAJ, Tolker-Nielsen T, Molin S (2007) Microbial motility involvement in biofilm structure formation - a 3-d modelling study
Water Science and Technology, 55(8-9):337-343.
images/2007_Wolf_BiotechnolBioeng.jpg
Wolf G, Picioreanu C, Van Loosdrecht MCM (2007) Kinetic modelling of photototrophic biofilms – the PHOBIA model
Biotechnology and Bioengineering, 97(5):1064-1079.
fig4b.jpg
Batstone DJ, Picioreanu C, Van Loosdrecht MCM (2006) Multidimensional modelling to investigate interspecies hydrogen transfer in anaerobic biofilms. Water Research, 40:3099-3108.
continuumEPS_discreteCells/HetAobNob_topdown_NO2&cells.jpg
Alpkvist E, Picioreanu C, Van Loosdrecht MCM, Heyden A (2006) Three-dimensional biofilm model with individual cells and continuum EPS matrix. 
Biotechnology and Bioengineering, 94(5):962-979.
Biofilm control Xavier JB, Picioreanu C, Rani SA, Van Loosdrecht MCM, Stewart PS (2005)
"Biofilm control strategies based on the enzymatic disruption of the EPS matrix – a modelling study"
Microbiology SGM (UK), 151:3817-3832.

Contains videos of the 3D biofilm simulations analyzed in the paper.

Biofilms in monolith reactors Ebrahimi S, Picioreanu C, Xavier JB, Kleerebezem R, Kreutzer M, Kapteijn F, Moulijn JA, Van Loosdrecht MCM (2005)
"Biofilm growth pattern in honeycomb monolith packings:
Effect of shear rate and substrate transport limitations"

Catalysis Today, 105(3-4):448-454.

Contains videos of the 2D biofilm simulations analyzed in the paper.

Excel snapshot
Pérez J, Picioreanu C, Van Loosdrecht MCM (2005)
"Modeling biofilm and floc diffusion processes based on analytical solution of reaction-diffusion equations"
Water Research, 39:1311-1323

Contains an MS Excel sheet with the calculation procedure used in the article.

framework Xavier JB, Picioreanu C, Van Loosdrecht MCM (2005)
"A Framework for Multidimensional Modelling of Activity and Structure of Multispecies Biofilms"
Environmental Microbiology 7(8):1085-1103

Contains videos of the 2D animations for the case study presented in the paper and link to the computer program described in the form of compiled java classes.

detachmentPaper Xavier JB, Picioreanu C, Van Loosdrecht MCM (2005)
"A general description of detachment for multidimensional modelling of biofilms"
Biotechnology and Bioengineering, 91(6):651-669

Contains videos of the 2D and 3D animations presented in the paper.

reactorsPaper Xavier JB, Picioreanu C, Van Loosdrecht MCM (2004)
"A modelling study of the activity and structure of biofilms in biological reactors"
Biofilms, 1(4):377-391

Contains videos of the 2D animations analyzed in the paper.

Anammox Picioreanu C, Kreft J-U, Van Loosdrecht MCM (2004)
"Particle-based multidimensional multispecies biofilm model"
Applied and Environmental Microbiology, 70(5),3024-3040.

Contains videos of the 2D and 3D animations for the case studies presented in the paper.

EST_2004 Martins AMP, Picioreanu C, Heijnen JJ and van Loosdrecht MCM (2004)
"Three-dimensional dual-morphotype species modeling of activated sludge flocs"
Environmental Science and Technology, 38:5632-5641.

Contains videos of the 3D animations for the case studies presented in the paper.
biocorrosion
Picioreanu C and van Loosdrecht MCM (2002)
"A mathematical model for initiation of microbiologically influenced corrosion by differential aeration"
Journal of the Electrochemical Society, 149(6):B211-B223.

Contains 2D animation for a case study presented in the paper.
posterBiocomplexity
Xavier JB, Picioreanu C, Van Loosdrecht MCM (2004)
Dynamic multidimensional modeling of structure and activity in multispecies biofilm systems - a particle-based approach

Electronic version of a poster presented at the Biocomplexity VI workshop (May 12-16, 2004, University of Indiana, Bloomington). This version contains several videos of simulations carried out with our biofilm modelling framework.
PDF version of the poster.



Other projects of biofilm modeling in our group include
Updated:  October 16, 2007  by  Cristian Picioreanu